PDB-8w6x: Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki...

ID or keywords:

Entry

Database: PDB / ID: 8w6x

Title

Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state

Components

(Periplasmic [NiFe] hydrogenase ...) x 2

Keywords

OXIDOREDUCTASE / Hydrogenase / NiFe complex / FeS cluster / Oxidized state

Function / homology

Function and homology information

cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...
Similarity search - Function

Biological species

Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.04 Å

Authors

Hiromoto, T. / Tamada, T.

Funding support

1items

Citation

Journal: Chem Sci / Year: 2023
Title: New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.
Authors: Hiromoto, T. / Nishikawa, K. / Inoue, S. / Ogata, H. / Hori, Y. / Kusaka, K. / Hirano, Y. / Kurihara, K. / Shigeta, Y. / Tamada, T. / Higuchi, Y.

History

Deposition	Aug 30, 2023	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Sep 13, 2023	ID: 7YW6
Revision 1.0	Sep 13, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8w6x.cif.gz	579 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8w6x_validation.pdf.gz	494.9 KB	Display	wwPDB validaton report
Full document	8w6x_full_validation.pdf.gz	495.7 KB	Display
Data in XML	8w6x_validation.xml.gz	20.3 KB	Display
Data in CIF	8w6x_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/8w6x ftp://data.pdbj.org/pub/pdb/validation_reports/w6/8w6x	HTTPS FTP

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Related structure data

Related structure data	4u9hS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (19) #144 - Dec 2011 Complex I similarity (3) #220 - Apr 2018 Dehalogenases similarity (2) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

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NCBI

Related items in Molecule of the Month

#111 - Mar 2009
Hydrogenase
similarity (19)
#144 - Dec 2011
Complex I
similarity (3)
#220 - Apr 2018
Dehalogenases
similarity (2)
#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

L: Periplasmic [NiFe] hydrogenase large subunit

S: Periplasmic [NiFe] hydrogenase small subunit

hetero molecules

90.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.705, 98.485, 126.860
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules LS

#1: Protein	Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain Mass: 59123.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) References: UniProt: P21852, cytochrome-c3 hydrogenase
#2: Protein	Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain Mass: 28676.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) References: UniProt: P21853, cytochrome-c3 hydrogenase

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Non-polymers , 8 types, 858 molecules

#3: Chemical	ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER Mass: 195.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃HFeN₂NiO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-OH / HYDROXIDE ION Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#9: Chemical	ChemComp-F3S / FE3-S4 CLUSTER Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₃S₄
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 842 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.5 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30%(v/v) 2-methyl-2,4-pentane-d12-diol, 10 mM glucose-d12, 25 mM Tris-d11-DCl in D2O

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	SPring-8	BL26B1		1	0.8
SPALLATION SOURCE	JPARC MLF	BL-03	J-PARC MLF BEAMLINE BL-03	2	1.8-5.8

Detector

Type	ID	Detector	Date
RAYONIX MX225HE	1	CCD	Apr 10, 2015
iBIX	2	DIFFRACTOMETER	Mar 21, 2015

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	LAUE	L	neutron	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.8	1
2	1.8	1
3	5.8	1

Reflection

Entry-ID: 8W6X

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_rim(I) all	Diffraction-ID	Net I/σ(I)
1.04-50	397623	99.9	8.5	1	0.059	0.062	1	19.7
2.2-20	38335	90.1	2.6	0.92	0.22	0.266	2	4.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID	% possible all
1.04-1.07	7.2	0.461	4.1	29097	0.924	0.496	1	99.6
2.2-2.32	2.8	0.394	2.3	5756	0.57	0.473	2	93.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472)	refinement
STARGazer		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

SU ML: 0.08 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 16.26 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4U9H

4u9h

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)	Refine-ID	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	Diffraction-ID	σ(F)
1.04-41.69	X-RAY DIFFRACTION	0.1474	0.1428	0.143	19868	397425	5	99.78	1	1.34
2.2-17.94	NEUTRON DIFFRACTION	0.2202	0.1893	0.1909	1893	38312	4.94	88.91	2	0

Refinement step

Cycle: LAST / Resolution: 1.04→41.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6188	0	106	842	7136

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	16618
X-RAY DIFFRACTION	f_angle_d	1.213	28273
X-RAY DIFFRACTION	f_dihedral_angle_d	18.819	4252
X-RAY DIFFRACTION	f_chiral_restr	0.095	1054
X-RAY DIFFRACTION	f_plane_restr	0.008	3027
NEUTRON DIFFRACTION	f_bond_d	0.014	16618
NEUTRON DIFFRACTION	f_angle_d	1.213	28273
NEUTRON DIFFRACTION	f_dihedral_angle_d	18.819	4252
NEUTRON DIFFRACTION	f_chiral_restr	0.095	1054
NEUTRON DIFFRACTION	f_plane_restr	0.008	3027

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.04-1.05	0.269	638	0.2515	12129	X-RAY DIFFRACTION	97
1.0514-1.0638	0.2518	658	0.2392	12486	X-RAY DIFFRACTION	100
1.0638-1.0768	0.2237	657	0.2328	12481	X-RAY DIFFRACTION	100
1.0768-1.0904	0.24	657	0.2177	12483	X-RAY DIFFRACTION	100
1.0904-1.1047	0.2264	657	0.2101	12499	X-RAY DIFFRACTION	100
1.1047-1.1199	0.2198	658	0.2041	12488	X-RAY DIFFRACTION	100
1.1199-1.1359	0.2023	657	0.1981	12496	X-RAY DIFFRACTION	100
1.1359-1.1528	0.2189	659	0.1995	12521	X-RAY DIFFRACTION	100
1.1528-1.1708	0.1992	658	0.1942	12504	X-RAY DIFFRACTION	100
1.1708-1.19	0.1898	661	0.189	12549	X-RAY DIFFRACTION	100
1.19-1.2106	0.1933	657	0.1907	12504	X-RAY DIFFRACTION	100
1.2106-1.2326	0.201	659	0.1878	12536	X-RAY DIFFRACTION	100
1.2326-1.2563	0.1822	661	0.1833	12549	X-RAY DIFFRACTION	100
1.2563-1.2819	0.1904	660	0.1791	12547	X-RAY DIFFRACTION	100
1.2819-1.3098	0.1953	659	0.1757	12532	X-RAY DIFFRACTION	100
1.3098-1.3403	0.1743	659	0.172	12558	X-RAY DIFFRACTION	100
1.3403-1.3738	0.1753	660	0.1716	12527	X-RAY DIFFRACTION	100
1.3738-1.4109	0.1717	660	0.165	12577	X-RAY DIFFRACTION	100
1.4109-1.4525	0.1639	663	0.159	12578	X-RAY DIFFRACTION	100
1.4525-1.4994	0.1676	662	0.1514	12592	X-RAY DIFFRACTION	100
1.4994-1.5529	0.153	663	0.1429	12600	X-RAY DIFFRACTION	100
1.5529-1.6151	0.1489	663	0.1396	12592	X-RAY DIFFRACTION	100
1.6151-1.6886	0.138	665	0.1356	12628	X-RAY DIFFRACTION	100
1.6886-1.7777	0.1301	665	0.131	12629	X-RAY DIFFRACTION	100
1.7777-1.889	0.1333	668	0.127	12695	X-RAY DIFFRACTION	100
1.889-2.0349	0.129	666	0.1257	12656	X-RAY DIFFRACTION	100
2.0349-2.2397	0.1239	672	0.1143	12745	X-RAY DIFFRACTION	100
2.2397-2.5637	0.1104	672	0.1073	12772	X-RAY DIFFRACTION	100
2.5637-3.2298	0.1084	676	0.1097	12843	X-RAY DIFFRACTION	100
3.23-41.69	0.133	698	0.133	13261	X-RAY DIFFRACTION	100
2.2-2.25	0.2928	133	0.2488	2560	NEUTRON DIFFRACTION	89
2.2547-2.3155	0.3132	142	0.248	2701	NEUTRON DIFFRACTION	93
2.3155-2.3835	0.252	137	0.2224	2690	NEUTRON DIFFRACTION	92
2.3835-2.4602	0.263	138	0.2161	2654	NEUTRON DIFFRACTION	93
2.4602-2.5479	0.2689	143	0.2165	2697	NEUTRON DIFFRACTION	93
2.5479-2.6496	0.2712	141	0.2126	2702	NEUTRON DIFFRACTION	94
2.6496-2.7698	0.2204	143	0.2041	2656	NEUTRON DIFFRACTION	91
2.7698-2.9153	0.2193	136	0.1887	2634	NEUTRON DIFFRACTION	91
2.9153-3.097	0.2112	131	0.1724	2574	NEUTRON DIFFRACTION	89
3.097-3.3348	0.1894	129	0.1588	2611	NEUTRON DIFFRACTION	89
3.3348-3.6678	0.1627	138	0.1427	2680	NEUTRON DIFFRACTION	92
3.6678-4.1926	0.1538	134	0.1335	2594	NEUTRON DIFFRACTION	88
4.1926-5.26	0.1542	135	0.1531	2458	NEUTRON DIFFRACTION	83
5.26-17.94	0.2278	113	0.2139	2208	NEUTRON DIFFRACTION	71

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Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules LS

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Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules LS

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